add_isoformAppends isoform annotation from UCSC isoforms file
 add_reflinkAppends isoform/name annotation from RefSeq/refLink
 add_xrefAppends name annotation from UCSC Xref file
 annotateAnnotates genomic positions based on a GTF model
 filterFilter annotations from a GTF file
 genesizeExtract genomic/transcript sizes for genes
 junctionsBuild a junction library from FASTA and GTF model
 queryQuery a GTF file by coordinates
 remove_dupRemoves "_dup" entries from a GTF file (experimental)


 fromgffConverts a GFF annotation file to GTF (experimental)
 tobedConvert a GFF/GTF file to BED format